ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-08-29T14:24:03+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/87Enhancing the display of a project search result2019-08-29T14:24:03+02:00Audrey GibertEnhancing the display of a project search resultI was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.I was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/86downloadsymlink, special characters2019-09-27T09:11:39+02:00Gerald Salingerald.salin@inra.frdownloadsymlink, special characterssome special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)some special characters are included in run names (e.g. /, (, )), introducing a bug in the download step (at least creating symlinks)V3.2.5Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/85Error addanalysis from graphic interface (firefox)2019-11-12T13:44:01+01:00Maxime MannoError addanalysis from graphic interface (firefox)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/84no template for BasicAnalyse2018-10-22T12:59:26+02:00Gerald Salingerald.salin@inra.frno template for BasicAnalysecf Maria.
The template does not exist
copy from BasicAnalysis.tplcf Maria.
The template does not exist
copy from BasicAnalysis.tplV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/83copy to clipboard from download windows does not work2020-06-11T17:09:25+02:00Gerald Salingerald.salin@inra.frcopy to clipboard from download windows does not work![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe w...![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe we have to upgrade the ZeroClipBoard.min.js file (3 yers old)Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/82Error downloading data with symlink and url2018-10-22T12:59:40+02:00Gerald Salingerald.salin@inra.frError downloading data with symlink and urlcan select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the ...can select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the browser a url prefix with http instead of httpsV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/80methyl_seq - template Bismark error displaying2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frmethyl_seq - template Bismark error displaying08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff2...08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff26100dfbb61200023b2.file.Bismark.tpl.php on line 159 and exactly 2 expected | ArgumentCountError thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/libs/plugins/modifier.get_description.php in line 177. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?id=55&tx_nG6_pi1%5Banalyze_id%5D=55299&tx_nG6_pi1%5Bproject_id%5D=7&tx_nG6_pi1%5Brun_id%5D=14200
![image](/uploads/1d71ea9dd0f07714692a5d1832293e27/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/79bug sending mail for purge demand while user disconnected2018-10-01T19:35:52+02:00Gerald Salingerald.salin@inra.frbug sending mail for purge demand while user disconnectedafter a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...after a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/78"Process mail demands" does not work with new version of typo32018-10-01T14:30:00+02:00Gerald Salingerald.salin@inra.fr"Process mail demands" does not work with new version of typo3no records found
delay_purge is not set in the ajax requestno records found
delay_purge is not set in the ajax requestV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/77Process mail demands : delay exceed always to "no"2018-10-01T14:30:06+02:00Gerald Salingerald.salin@inra.frProcess mail demands : delay exceed always to "no"whereas we know some have delay exceededwhereas we know some have delay exceededV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/76Admin > Statisctis does not work2018-10-01T13:04:35+02:00Gerald Salingerald.salin@inra.frAdmin > Statisctis does not work> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-s...> 01-10-18 10:54 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function split() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/class.tx_nG6_eid.php in line 808. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=project_distribution&by=title&role=create_user&values=BIA,Bioinfo%20GENOTOULV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/75bug in purge management2018-10-01T13:04:43+02:00Gerald Salingerald.salin@inra.frbug in purge managementpurge management doe not work with new versio of typo3purge management doe not work with new versio of typo3V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/74ONT-QC bug with l502019-01-04T17:45:19+01:00Maxime MannoONT-QC bug with l50we removed the L50 from the R script, and the workflow need this informationwe removed the L50 from the R script, and the workflow need this informationV3.2.2Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/73problem with gzip 1.5 and 1.9 on the new cluster2018-09-17T09:17:48+02:00Gerald Salingerald.salin@inra.frproblem with gzip 1.5 and 1.9 on the new clusterafter some hours of debugging, we found the 1.5 and 1.9 version of gzip implies problem with the server load. huge peaks (> 1000 of load average) were observed and reproduced in the case of massive jobs using system gzip (on the new slur...after some hours of debugging, we found the 1.5 and 1.9 version of gzip implies problem with the server load. huge peaks (> 1000 of load average) were observed and reproduced in the case of massive jobs using system gzip (on the new slurm cluster).
It was not observed with the sge cluster, using version 1.3.
installing 1.3 gzip version on the new cluster solved the problem, but we have to use get_exec_path("gzip") in the components instead of gzip command lineV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/72purge error if directory has a lot of files and folders2018-09-17T09:19:33+02:00Gerald Salingerald.salin@inra.frpurge error if directory has a lot of files and foldersreplace ls $dir | xargs rm -f with find . -exec rm -f {}replace ls $dir | xargs rm -f with find . -exec rm -f {}V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/71clean pipeline outputs if succeeded2018-09-06T15:09:01+02:00Gerald Salingerald.salin@inra.frclean pipeline outputs if succeededallow the deletion of files in the worflow output dir to save dik spaceallow the deletion of files in the worflow output dir to save dik spaceV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/70enhance disk usage with concatenatefilesgroups2018-09-17T09:30:51+02:00Gerald Salingerald.salin@inra.frenhance disk usage with concatenatefilesgroupsto limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles com...to limit the disk usage in illumina pipelines, do not store the output of ConcatenateFilesGroups component in its out output folder, but rather in the run.get_work_directory() folder.
saves a copy step (originally done in AddRawFiles componenent) and limit the disk usage (can represent few hundreds of Gb for novaseq runs)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/69Add a super admin ng6 who can see all projects2019-09-27T13:14:15+02:00Claire KuchlyAdd a super admin ng6 who can see all projectshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/68add md5sum for raw data in all pipelines2018-09-07T12:07:23+02:00Gerald Salingerald.salin@inra.fradd md5sum for raw data in all pipelinesV3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/67jflow server not reachable with https2018-09-17T09:30:12+02:00Gerald Salingerald.salin@inra.frjflow server not reachable with httpsaccessing ng6-slurm with https make the jflow server not accessible due to security reason (accessing http://ng6-slurm:8080)
changing to https://ng6-slurm:8080 does not solve the problem...another one is raisedaccessing ng6-slurm with https make the jflow server not accessible due to security reason (accessing http://ng6-slurm:8080)
changing to https://ng6-slurm:8080 does not solve the problem...another one is raisedV3.2 - Slurm